Merge pull request #643 from mrariden/export_rois

Export ROIs directly to ImageJ

cellpose/__main__.py

@@ -20,7 +20,7 @@
 
 import logging
 
-
+# settings re-grouped a bit
 def main():
     """ Run cellpose from command line
     """
@@ -178,6 +178,8 @@ def main():
                                   save_flows=args.save_flows,save_outlines=args.save_outlines,
                                   save_ncolor=args.save_ncolor,dir_above=args.dir_above,savedir=args.savedir,
                                   save_txt=args.save_txt,in_folders=args.in_folders)
+                if args.save_rois:
+                    io.save_rois(masks, image_name)
             logger.info('>>>> completed in %0.3f sec'%(time.time()-tic))
         else:
 

cellpose/cli.py

@@ -106,6 +106,8 @@ def get_arg_parser():
                              help='whether or not to save RGB images of flows when masks are saved (disabled by default)')
     output_args.add_argument('--save_outlines', action='store_true',
                              help='whether or not to save RGB outline images when masks are saved (disabled by default)')
+    output_args.add_argument('--save_rois', action='store_true',
+                             help='whether or not to save ImageJ compatible ROI archive (disabled by default)')
     output_args.add_argument('--save_ncolor', action='store_true',
                              help='whether or not to save minimal "n-color" masks (disabled by default')
     output_args.add_argument('--save_txt', action='store_true',

cellpose/gui/gui.py

@@ -1835,6 +1835,7 @@ def enable_buttons(self):
         self.saveFlows.setEnabled(True)
         self.saveServer.setEnabled(True)
         self.saveOutlines.setEnabled(True)
+        self.saveROIs.setEnabled(True)
         self.toggle_mask_ops()
 
         self.update_plot()

cellpose/gui/guiparts.py

@@ -279,8 +279,14 @@ def __init__(self, parent=None):
             <li class="has-line-data" data-line-start="12" data-line-end="13">Start draw mask = right-click</li>
             <li class="has-line-data" data-line-start="13" data-line-end="15">End draw mask = right-click, or return to circle at beginning</li>
             </ul>
-            <p class="has-line-data" data-line-start="15" data-line-end="16">Overlaps in masks are NOT allowed. If you draw a mask on top of another mask, it is cropped so that it doesn’t overlap with the old mask. Masks in 2D should be single strokes (single stroke is checked). If you want to draw masks in 3D (experimental), then you can turn this option off and draw a stroke on each plane with the cell and then press ENTER. 3D labelling will fill in planes that you have not labelled so that you do not have to as densely label.</p>
-            <p class="has-line-data" data-line-start="17" data-line-end="18">!NOTE!: The GUI automatically saves after you draw a mask in 2D but NOT after 3D mask drawing and NOT after segmentation. Save in the file menu or with Ctrl+S. The output file is in the same folder as the loaded image with <code>_seg.npy</code> appended.</p>
+            <p class="has-line-data" data-line-start="15" data-line-end="16">Overlaps in masks are NOT allowed. If you \
+            draw a mask on top of another mask, it is cropped so that it doesn’t overlap with the old mask. Masks in 2D \
+            should be single strokes (single stroke is checked). If you want to draw masks in 3D (experimental), then \
+            you can turn this option off and draw a stroke on each plane with the cell and then press ENTER. 3D \
+            labelling will fill in planes that you have not labelled so that you do not have to as densely label.</p>
+            <p class="has-line-data" data-line-start="17" data-line-end="18">!NOTE!: The GUI automatically saves after \
+            you draw a mask in 2D but NOT after 3D mask drawing and NOT after segmentation. Save in the file menu or \
+            with Ctrl+S. The output file is in the same folder as the loaded image with <code>_seg.npy</code> appended.</p>
             <table class="table table-striped table-bordered">
             <br><br>
             FYI there are tooltips throughout the GUI (hover over text to see)
@@ -329,6 +335,18 @@ def __init__(self, parent=None):
             <td>load masks file (must be same size as image with 0 for NO mask, and 1,2,3… for masks)</td>
             </tr>
             <tr>
+            <td>CTRL+N</td>
+            <td>save masks as PNG</td>
+            </tr>
+            <tr>
+            <td>CTRL+R</td>
+            <td>save ROIs to native ImageJ ROI format</td>
+            </tr>
+            <tr>
+            <td>CTRL+F</td>
+            <td>save flows to image file</td>
+            </tr>
+            <tr>
             <td>A/D or LEFT/RIGHT</td>
             <td>cycle through images in current directory</td>
             </tr>

cellpose/gui/io.py

@@ -7,7 +7,7 @@
 import fastremap 
 
 from .. import utils, plot, transforms, models
-from ..io import imread, imsave, outlines_to_text, add_model, remove_model
+from ..io import imread, imsave, outlines_to_text, add_model, remove_model, save_rois
 from ..transforms import normalize99
 
 try:
@@ -452,7 +452,15 @@ def _save_flows(parent):
     if len(parent.flows) > 0:
         imsave(base + '_cp_flows.tif', parent.flows[4][:-1])
         imsave(base + '_cp_cellprob.tif', parent.flows[4][-1])
-
+
+def _save_rois(parent):
+    """ save masks as rois in .zip file for ImageJ """
+    filename = parent.filename
+    if parent.NZ == 1:
+        print(f'GUI_INFO: saving {parent.cellpix[0].max()} ImageJ ROIs to .zip archive.')
+        save_rois(parent.cellpix[0], parent.filename)
+    else:
+        print('ERROR: cannot save 3D outlines')
 
 def _save_outlines(parent):
     filename = parent.filename

cellpose/gui/menus.py

@@ -46,6 +46,12 @@ def mainmenu(parent):
     file_menu.addAction(parent.saveOutlines)
     parent.saveOutlines.setEnabled(False)
 
+    parent.saveROIs = QAction("Save outlines as .zip archive of &ROI files for ImageJ", parent)
+    parent.saveROIs.setShortcut("Ctrl+R")
+    parent.saveROIs.triggered.connect(lambda: io._save_rois(parent))
+    file_menu.addAction(parent.saveROIs)
+    parent.saveROIs.setEnabled(False)
+
     parent.saveFlows = QAction("Save &Flows and cellprob as tif", parent)
     parent.saveFlows.setShortcut("Ctrl+F")
     parent.saveFlows.triggered.connect(lambda: io._save_flows(parent))

cellpose/io.py

@@ -7,6 +7,7 @@
 from tqdm import tqdm
 from pathlib import Path
 from . import version_str
+from roifile import ImagejRoi, roiwrite
 
 
 try:
@@ -379,6 +380,34 @@ def save_to_png(images, masks, flows, file_names):
     """
     save_masks(images, masks, flows, file_names, png=True)
 
+
+def save_rois(masks, file_name):
+    """ save masks to .roi files in .zip archive for ImageJ/Fiji
+
+    Parameters
+    ----------
+
+    masks: 2D array, int
+        masks output from Cellpose.eval, where 0=NO masks; 1,2,...=mask labels
+
+    file_name: str
+        name to save the .zip file to
+
+    -------
+
+    """
+    outlines = utils.outlines_list(masks)
+    rois = [ImagejRoi.frompoints(outline) for outline in outlines]
+    file_name = os.path.splitext(file_name)[0] + '_rois.zip'
+
+    # Delete file if it exists; the roifile lib appends to existing zip files.
+    # If the user removed a mask it will still be in the zip file
+    if os.path.exists(file_name):
+        os.remove(file_name)
+
+    roiwrite(file_name, rois)
+
+
 # Now saves flows, masks, etc. to separate folders.
 def save_masks(images, masks, flows, file_names, png=True, tif=False, channels=[0,0],
                suffix='',save_flows=False, save_outlines=False, save_ncolor=False, 

docs/gui.rst

@@ -152,6 +152,12 @@ Keyboard shortcuts
 | CTRL+M              | load masks file (must be same size as image   |
 |                     | with 0 for NO mask, and 1,2,3... for masks)   |
 +---------------------+-----------------------------------------------+
+| CTRL+N              | save masks as PNG                             |
++---------------------+-----------------------------------------------+
+| CTRL+R              | save ROIs to native ImageJ ROI format         |
++---------------------+-----------------------------------------------+
+| CTRL+F              | save flows to image file                      |
++---------------------+-----------------------------------------------+
 | A/D or LEFT/RIGHT   | cycle through images in current directory     |
 +---------------------+-----------------------------------------------+
 | W/S or UP/DOWN      | change color (RGB/gray/red/green/blue)        |

docs/index.rst

@@ -16,7 +16,7 @@ Also check out these resources:
 Cellpose 2.0
 
 - `paper <https://www.biorxiv.org/content/10.1101/2022.04.01.486764v1>`_ on biorxiv
-- `talk <https://www.youtube.com/watch?v=3ydtAhfq6H0`_ 
+- `talk <https://www.youtube.com/watch?v=3ydtAhfq6H0>`_
 - twitter `thread <https://twitter.com/marius10p/status/1511415409047650307?s=20&t=umTVIG1CFKIWHYMrQqFKyQ>`_
 - human-in-the-loop training protocol `video <https://youtu.be/3Y1VKcxjNy4>`_
 

docs/outputs.rst

@@ -65,7 +65,31 @@ Or use the function below if running in a notebook
     from cellpose import io
     io.save_to_png(images, masks, flows, image_names)
 
-ROI manager compatible output for ImageJ
+Native ImageJ ROI archive output
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+You can save the outlines of the ROIs in a ImageJ-native ROI archive file. Rather than using the legacy solution below,
+you can use this function to create an ROI archive file that can be opened in directly in ImageJ. Recent versions of
+ImageJ can autodetect the file format. Open in ImageJ using File > Open... and select the file.
+The ROIs will appear in the ROI manager.
+
+To save the outlines using the CLI use the flag ``--save_rois``.
+
+To save the outlines using the API use the ``save_rois`` function in ``io.py``:
+
+This function is also available in the GUI.
+
+::
+
+    from cellpose import io, utils
+
+    # image_name is file name of image
+    # masks is numpy array of masks for image
+    io.save_rois(masks, '<your_filename_string>')
+
+    # the file will be saved as '<your_filename_string>_rois.zip'
+
+
+(Legacy ImageJ Interface) ROI manager compatible output for ImageJ
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 You can save the outlines of ROIs in a text file that's compatible with ImageJ 

environment.yml

@@ -17,5 +17,6 @@ dependencies:
     - tifffile
     - fastremap
     - cellpose
+    - roifile
 
 

setup.py

@@ -8,7 +8,8 @@
                 'torch>=1.6',
                 'opencv-python-headless',
                 'fastremap',
-                'imagecodecs'
+                'imagecodecs',
+                'roifile',
                 ]
 
 gui_deps = [